The development of the Visual-Perceptual Chemistry Specific (VPCS) assessment tool is based on items that align to eight visual-perceptual skills considered as needed by chemistry students. This tool includes a comprehensive range of visual operations and presents items within a chemistry context without requiring content knowledge to solve correctly. The VPCS was administrated to a total of 2,713 chemistry students taking general, organic, inorganic, and physical chemistry courses at a large, southeastern university over a period of three academic years. The preliminary validation process involved primarily factor analysis and Item Response Theory. A three-factor solution was considered appropriate with the most reasonable interpretation labeling Factor 1 as a general visual-spatial skill, Factor 2 involving multiple viewpoints (frames of reference), and Factor 3 related to memory ability. Our analysis supports an interpretation relevant to chemistry instruction that departs from previous findings where the factors obtained were viewed in terms of static or kinetic qualities (mechanical) and/or two-dimensional versus three-dimensional aspects. Several interpretations for the three-factor solution are discussed as well as implications for teaching and future research.